# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun 12 14:45:04 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3N)[C@@H]2O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 827  827  '(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside'  ligand  71  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_827
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 827  C13  C  CH1   0   0.279  -3.0483   1.2573  -0.3060
 827  C15  C  CH1   0  -0.031  -4.5870  -0.4717  -0.8925
 827  C20  C  CH1   0   0.038  -5.2896   1.2532   0.7965
 827  C22  C  CH1   0  -0.145  -4.1570   2.1302   0.2821
 827  C24  C  CH1   0  -0.103  -1.4742  -1.4291   1.5943
 827  C02  C  CT    0   0.150   5.1008   1.4621  -1.0242
 827  C04  C  CH2   0  -0.192   3.6639   1.6119  -1.5192
 827  C06  C  CH1   0   0.199   3.0893  -0.6338  -1.0675
 827  C11  C  CH1   0   0.059  -1.4669  -0.4258   0.4415
 827  C18  C  CH1   0  -0.003  -5.7642   0.3084  -0.3016
 827  C27  C  CH1   0  -0.100   0.9469  -1.9845   1.1498
 827  C09  C  CH1   0   0.025  -0.0706   0.1769   0.2979
 827  C31  C  CH1   0  -0.083   5.1533   0.3330   0.0229
 827  C16  C  CH2   0  -0.163  -4.9946  -1.2579  -2.1191
 827  O14  O  O2    0  -0.505  -3.5621   0.4236  -1.3002
 827  O12  O  O2    0  -0.524  -2.4427   0.5551   0.7445
 827  C26  C  CH2   0  -0.469  -0.4659  -2.5328   1.3070
 827  C08  C  CH1   0   0.043   0.9682  -0.9224   0.0576
 827  O10  O  OH1   0  -0.665  -0.0768   1.0852  -0.7765
 827  O07  O  O2    0  -0.523   2.2431  -0.3137   0.0012
 827  C29  C  CH1   0   0.071   4.4930  -0.9363  -0.5309
 827  O05  O  O2    0  -0.489   3.1199   0.4006  -2.0050
 827  O03  O  OH1   0  -0.679   5.9470   1.0566  -2.0883
 827  N32  N  NH1   0  -0.606   6.4970   0.0350   0.4850
 827  C33  C  CH3   0  -0.525   6.8167   0.4965   1.8181
 827  O30  O  OH1   0  -0.717   4.4844  -1.9401   0.4443
 827  N28  N  NH2   0  -0.816   1.9470  -3.0048   0.8578
 827  N25  N  NH2   0  -0.795  -2.7970  -2.0077   1.7563
 827  N23  N  NH2   0  -0.801  -3.6419   2.9766   1.3424
 827  O21  O  OH1   0  -0.674  -6.3320   2.1013   1.2215
 827  O19  O  OH1   0  -0.675  -6.7227  -0.5599   0.2674
 827  H1   H  HCH1  0   0.237  -2.3218   1.8912  -0.8217
 827  H2   H  HCH1  0   0.239  -4.2057  -1.1740  -0.1396
 827  H3   H  HCH1  0   0.208  -4.9138   0.6573   1.6417
 827  H4   H  HCH1  0   0.222  -4.5493   2.7087  -0.5704
 827  H5   H  HCH1  0   0.207  -1.1405  -0.8974   2.5010
 827  H6   H  HCH2  0   0.205   3.0477   2.0331  -0.7144
 827  H7   H  HCH2  0   0.243   3.6261   2.3198  -2.3513
 827  H8   H  HCH1  0   0.242   2.7005  -1.5066  -1.6065
 827  H9   H  HCH1  0   0.229  -1.7307  -0.9581  -0.4820
 827  H11  H  HCH1  0   0.216  -6.2159   0.9196  -1.0969
 827  H12  H  HCH1  0   0.244   1.2435  -1.5085   2.0908
 827  H13  H  HCH1  0   0.209   0.1814   0.6893   1.2396
 827  H14  H  HCH1  0   0.229   4.5575   0.6665   0.8815
 827  H18  H  HCH2  0   0.195  -5.8570  -1.8848  -1.8605
 827  H19  H  HCH2  0   0.197  -5.3284  -0.5599  -2.9002
 827  H20  H  HCH2  0   0.251  -0.4793  -3.2647   2.1196
 827  H21  H  HCH2  0   0.228  -0.7640  -3.0641   0.3961
 827  H22  H  HCH1  0   0.224   0.7304  -1.3990  -0.9062
 827  H23  H  HOH1  0   0.454   0.7873   1.5067  -0.8209
 827  H24  H  HCH1  0   0.191   5.0812  -1.2711  -1.3979
 827  H25  H  HOH1  0   0.449   6.0703   1.8010  -2.6873
 827  H26  H  HNH1  0   0.343   7.1818   0.3629  -0.1819
 827  H28  H  HCH3  0   0.192   6.6723   1.5721   1.9882
 827  H29  H  HCH3  0   0.221   6.2067  -0.0337   2.5515
 827  H30  H  HCH3  0   0.227   7.8597   0.2677   2.0396
 827  H31  H  HOH1  0   0.466   3.5729  -2.3017   0.5714
 827  H32  H  HNH2  0   0.373   2.0291  -3.6381   1.6448
 827  H33  H  HNH2  0   0.360   1.6458  -3.5743   0.0739
 827  H35  H  HNH2  0   0.349  -2.7678  -2.6854   2.5088
 827  H36  H  HNH2  0   0.351  -3.4420  -1.2910   2.0627
 827  H38  H  HNH2  0   0.345  -2.8822   3.5404   0.9801
 827  H39  H  HNH2  0   0.348  -4.3602   3.6367   1.6108
 827  H41  H  HOH1  0   0.450  -7.0225   1.5539   1.6089
 827  H42  H  HOH1  0   0.459  -7.3722  -0.7930  -0.4012
 827  O17  O  OH1   0  -0.667  -3.9044  -2.0396  -2.5455
 827  C01  C  CH3   0  -0.686   5.5617   2.7960  -0.4484
 827  H10  H  HOH1  0   0.455  -4.1704  -2.5097  -3.3407
 827  H15  H  HCH3  0   0.238   5.4859   3.5872  -1.1987
 827  H16  H  HCH3  0   0.233   4.9545   3.0946   0.4065
 827  H17  H  HCH3  0   0.244   6.6009   2.7484  -0.1237

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 827  N28  C27  single  1.458  0.020  1.458
 827  O30  C29  single  1.400  0.020  1.400
 827  C27  C26  single  1.524  0.020  1.524
 827  C27  C08  single  1.524  0.020  1.524
 827  C26  C24  single  1.522  0.020  1.522
 827  C29  C06  single  1.533  0.020  1.533
 827  C29  C31  single  1.534  0.020  1.534
 827  N32  C33  single  1.447  0.020  1.447
 827  N32  C31  single  1.452  0.020  1.452
 827  C06  O07  single  1.400  0.020  1.400
 827  C06  O05  single  1.396  0.020  1.396
 827  O07  C08  single  1.414  0.020  1.414
 827  C24  N25  single  1.453  0.020  1.453
 827  C24  C11  single  1.528  0.020  1.528
 827  C08  C09  single  1.531  0.020  1.531
 827  C31  C02  single  1.541  0.020  1.541
 827  O05  C04  single  1.414  0.020  1.414
 827  C09  C11  single  1.528  0.020  1.528
 827  C09  O10  single  1.407  0.020  1.407
 827  C11  O12  single  1.416  0.020  1.416
 827  C02  O03  single  1.419  0.020  1.419
 827  C02  C04  single  1.527  0.020  1.527
 827  C02  C01  single  1.524  0.020  1.524
 827  O12  C13  single  1.401  0.020  1.401
 827  C16  C15  single  1.513  0.020  1.513
 827  C16  O17  single  1.408  0.020  1.408
 827  O14  C15  single  1.421  0.020  1.421
 827  O14  C13  single  1.396  0.020  1.396
 827  C15  C18  single  1.531  0.020  1.531
 827  C13  C22  single  1.529  0.020  1.529
 827  C18  C20  single  1.524  0.020  1.524
 827  C18  O19  single  1.413  0.020  1.413
 827  C22  C20  single  1.522  0.020  1.522
 827  C22  N23  single  1.451  0.020  1.451
 827  C20  O21  single  1.409  0.020  1.409
 827  C13  H1   single  0.970  0.020  1.090
 827  C15  H2   single  0.970  0.020  1.090
 827  C20  H3   single  0.970  0.020  1.090
 827  C22  H4   single  0.970  0.020  1.090
 827  C24  H5   single  0.970  0.020  1.090
 827  C04  H6   single  0.970  0.020  1.090
 827  C04  H7   single  0.970  0.020  1.090
 827  C06  H8   single  0.970  0.020  1.090
 827  C11  H9   single  0.970  0.020  1.090
 827  O17  H10  single  0.850  0.020  0.980
 827  C18  H11  single  0.970  0.020  1.090
 827  C27  H12  single  0.970  0.020  1.090
 827  C09  H13  single  0.970  0.020  1.090
 827  C31  H14  single  0.970  0.020  1.090
 827  C01  H15  single  0.970  0.020  1.090
 827  C01  H16  single  0.970  0.020  1.090
 827  C01  H17  single  0.970  0.020  1.090
 827  C16  H18  single  0.970  0.020  1.090
 827  C16  H19  single  0.970  0.020  1.090
 827  C26  H20  single  0.970  0.020  1.090
 827  C26  H21  single  0.970  0.020  1.090
 827  C08  H22  single  0.970  0.020  1.090
 827  O10  H23  single  0.850  0.020  0.980
 827  C29  H24  single  0.970  0.020  1.090
 827  O03  H25  single  0.850  0.020  0.980
 827  N32  H26  single  0.890  0.020  1.040
 827  C33  H28  single  0.970  0.020  1.090
 827  C33  H29  single  0.970  0.020  1.090
 827  C33  H30  single  0.970  0.020  1.090
 827  O30  H31  single  0.850  0.020  0.980
 827  N28  H32  single  0.890  0.020  1.040
 827  N28  H33  single  0.890  0.020  1.040
 827  N25  H35  single  0.890  0.020  1.040
 827  N25  H36  single  0.890  0.020  1.040
 827  N23  H38  single  0.890  0.020  1.040
 827  N23  H39  single  0.890  0.020  1.040
 827  O21  H41  single  0.850  0.020  0.980
 827  O19  H42  single  0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 827  H1   C13  O12  110.91  3.000
 827  H1   C13  O14  104.77  3.000
 827  O12  C13  O14  113.19  3.000
 827  H1   C13  C22  109.41  3.000
 827  O14  C13  C22  110.37  3.000
 827  O12  C13  C22  108.14  3.000
 827  H2   C15  O14  110.45  3.000
 827  H2   C15  C16  108.49  3.000
 827  O14  C15  C16  106.81  3.000
 827  H2   C15  C18  109.16  3.000
 827  O14  C15  C18  110.14  3.000
 827  C16  C15  C18  111.75  3.000
 827  H3   C20  O21  110.30  3.000
 827  H3   C20  C18  108.90  3.000
 827  O21  C20  C18  111.09  3.000
 827  H3   C20  C22  108.51  3.000
 827  O21  C20  C22  107.80  3.000
 827  C18  C20  C22  110.20  3.000
 827  H4   C22  N23  112.66  3.000
 827  H4   C22  C20  107.39  3.000
 827  N23  C22  C20  110.68  3.000
 827  H4   C22  C13  105.09  3.000
 827  N23  C22  C13  110.90  3.000
 827  C20  C22  C13  109.92  3.000
 827  H5   C24  N25  112.08  3.000
 827  H5   C24  C26  107.72  3.000
 827  N25  C24  C26  109.59  3.000
 827  H5   C24  C11  107.59  3.000
 827  N25  C24  C11  110.48  3.000
 827  C26  C24  C11  109.29  3.000
 827  O03  C02  C01  110.68  3.000
 827  C01  C02  C31  111.98  3.000
 827  O03  C02  C31  106.26  3.000
 827  C01  C02  C04  108.73  3.000
 827  O03  C02  C04  110.25  3.000
 827  C31  C02  C04  108.92  3.000
 827  H7   C04  H6   106.87  3.000
 827  H7   C04  O05  106.26  3.000
 827  H6   C04  O05  111.38  3.000
 827  H7   C04  C02  110.05  3.000
 827  H6   C04  C02  109.17  3.000
 827  O05  C04  C02  112.91  3.000
 827  H8   C06  O05  105.50  3.000
 827  H8   C06  C29  109.85  3.000
 827  O05  C06  C29  111.17  3.000
 827  H8   C06  O07  110.04  3.000
 827  O05  C06  O07  110.88  3.000
 827  C29  C06  O07  109.35  3.000
 827  H9   C11  O12  110.49  3.000
 827  H9   C11  C09  109.38  3.000
 827  O12  C11  C09  112.12  3.000
 827  H9   C11  C24  108.37  3.000
 827  O12  C11  C24  106.86  3.000
 827  C09  C11  C24  109.53  3.000
 827  H11  C18  O19  110.73  3.000
 827  H11  C18  C20  107.72  3.000
 827  O19  C18  C20  107.58  3.000
 827  H11  C18  C15  108.65  3.000
 827  O19  C18  C15  111.34  3.000
 827  C20  C18  C15  110.77  3.000
 827  H12  C27  N28  106.88  3.000
 827  H12  C27  C08  108.00  3.000
 827  N28  C27  C08  109.55  3.000
 827  H12  C27  C26  108.59  3.000
 827  C08  C27  C26  109.74  3.000
 827  N28  C27  C26  113.88  3.000
 827  H13  C09  O10  110.71  3.000
 827  H13  C09  C08  108.24  3.000
 827  O10  C09  C08  110.28  3.000
 827  H13  C09  C11  108.20  3.000
 827  O10  C09  C11  108.81  3.000
 827  C08  C09  C11  110.58  3.000
 827  H14  C31  N32  108.42  3.000
 827  H14  C31  C29  107.48  3.000
 827  N32  C31  C29  110.08  3.000
 827  H14  C31  C02  106.90  3.000
 827  N32  C31  C02  113.47  3.000
 827  C29  C31  C02  110.26  3.000
 827  H19  C16  H18  106.95  3.000
 827  H19  C16  O17  111.87  3.000
 827  H18  C16  O17  111.28  3.000
 827  H19  C16  C15  109.14  3.000
 827  H18  C16  C15  108.52  3.000
 827  O17  C16  C15  109.00  3.000
 827  C15  O14  C13  115.95  3.000
 827  C11  O12  C13  118.98  3.000
 827  H21  C26  H20  106.85  3.000
 827  H21  C26  C27  109.94  3.000
 827  H20  C26  C27  109.20  3.000
 827  H21  C26  C24  109.16  3.000
 827  H20  C26  C24  109.69  3.000
 827  C27  C26  C24  111.88  3.000
 827  H22  C08  O07  110.25  3.000
 827  H22  C08  C09  107.55  3.000
 827  O07  C08  C09  107.99  3.000
 827  H22  C08  C27  108.82  3.000
 827  C09  C08  C27  112.24  3.000
 827  O07  C08  C27  109.96  3.000
 827  H23  O10  C09  108.30  3.000
 827  C08  O07  C06  118.49  3.000
 827  H24  C29  O30  109.53  3.000
 827  H24  C29  C31  107.83  3.000
 827  O30  C29  C31  110.15  3.000
 827  H24  C29  C06  105.90  3.000
 827  C31  C29  C06  110.93  3.000
 827  O30  C29  C06  112.33  3.000
 827  C06  O05  C04  114.35  3.000
 827  H25  O03  C02  108.77  3.000
 827  H26  N32  C33  110.79  3.000
 827  H26  N32  C31  110.52  3.000
 827  C33  N32  C31  115.62  3.000
 827  H30  C33  H29  107.23  3.000
 827  H30  C33  H28  107.44  3.000
 827  H29  C33  H28  107.35  3.000
 827  H30  C33  N32  109.37  3.000
 827  H29  C33  N32  109.93  3.000
 827  H28  C33  N32  115.21  3.000
 827  H31  O30  C29  110.95  3.000
 827  H33  N28  H32  105.86  3.000
 827  H33  N28  C27  110.11  3.000
 827  H32  N28  C27  109.71  3.000
 827  H36  N25  H35  105.50  3.000
 827  H36  N25  C24  109.40  3.000
 827  H35  N25  C24  108.84  3.000
 827  H39  N23  H38  105.32  3.000
 827  H39  N23  C22  108.80  3.000
 827  H38  N23  C22  109.23  3.000
 827  H41  O21  C20  108.04  3.000
 827  H42  O19  C18  109.11  3.000
 827  H10  O17  C16  107.93  3.000
 827  H17  C01  H16  108.03  3.000
 827  H17  C01  H15  107.59  3.000
 827  H16  C01  H15  107.54  3.000
 827  H17  C01  C02  111.26  3.000
 827  H16  C01  C02  111.56  3.000
 827  H15  C01  C02  110.68  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 827  Var_01  H6   C04  O05  C06  -64.08  30.0  1
 827  Var_02  H28  C33  N32  C31  -55.88  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 827  chir_01  C13  O12  O14  C22  negativ
 827  chir_02  C15  O14  C16  C18  positiv
 827  chir_03  C20  O21  C18  C22  negativ
 827  chir_04  C22  N23  C20  C13  positiv
 827  chir_05  C24  N25  C26  C11  negativ
 827  chir_06  C02  C31  C04  C01  negativ
 827  chir_07  C06  O05  O07  C29  positiv
 827  chir_08  C11  O12  C24  C09  positiv
 827  chir_09  C18  O19  C15  C20  positiv
 827  chir_10  C27  N28  C26  C08  positiv
 827  chir_11  C09  O10  C11  C08  negativ
 827  chir_12  C31  C29  N32  C02  negativ
 827  chir_13  C08  O07  C09  C27  positiv
 827  chir_14  C29  O30  C06  C31  negativ

